library(tidyverse)
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-- Attaching packages ---------------------------------------------------------------------- tidyverse 1.3.1 --
√ ggplot2 3.3.5     √ purrr   0.3.4
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library(tuneR)
library(devtools)
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library(class)
library(cvTools)
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library(randomForest)
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Type rfNews() to see new features/changes/bug fixes.

Attaching package: ‘randomForest’

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library(GEOquery) 
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Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages 'citation("pkgname")'.


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library(R.utils)
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library(viridis)
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gse36059 = getGEO("GSE36059")[[1]]
Found 1 file(s)
GSE36059_series_matrix.txt.gz
|--------------------------------------------------|
|==================================================|
gse48581 = getGEO("GSE48581")[[1]]
Found 1 file(s)
GSE48581_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz 
gse129166 = getGEO("GSE129166")[[1]]
Found 1 file(s)
GSE129166_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz 
gse15296 = getGEO("GSE15296")[[1]]
Found 1 file(s)
GSE15296_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz 
gse36074_f = fData(gse36059)
gse36074_f
gse36074_f = fData(gse48581)
gse36074_f
gse129166_f = fData(gse129166)
gse129166_f
gse15296_f = fData(gse15296)
gse15296_f
gse36074_p = pData(gse36059)
gse36074_p
gse48581_p = pData(gse48581)
gse48581_p
gse129166_p = pData(gse129166)
gse129166_p
gse15296_p = pData(gse15296)
gse15296_p
data.frame(ifelse(gse36074_p$characteristics_ch1) == "diagnosis: non-rejecting", 0, 1)

Main outcomes are non-rejecting, TCMR (acute T-cell–mediated rejection), ABMR (anti-donor antibody-mediated rejection), and MIXED. Also has nephrectomy.

gse36074_ex = data.frame(t(exprs(gse36059)))
gse36074_ex
gse48581_ex = data.frame(t(exprs(gse48581)))
gse48581_ex
gse129166_ex = data.frame(t(exprs(gse129166)))
gse129166_ex
gse15296_ex = data.frame(t(exprs(gse15296)))
gse15296_ex
start = 1
stop = 100
boxplot(gse36074_ex[start:stop])

boxplot(gse48581_ex[start:stop])

boxplot(gse129166_ex[start:stop])

boxplot(gse15296_ex[start:stop])

merge(gse36074_ex, gse48581_ex, all = TRUE)
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